The burden and behaviour of influenza in Southeast Asia is poorly characterised, leading to uncertainty about the importance of influenza as a local health problem and the role of Southeast Asia in the global epidemiology of influenza. Prospective community-based studies have provided fundamental insights into the epidemiology of influenza in temperate regions; therefore a household-based cohort study was established with the aim of determining the intensity and characteristics of influenza transmission in a semi-rural tropical setting. The primary results of the cohort study are presented, along with the results of a survey of social contact patterns in the cohort and a mathematical model of the spread of pandemic influenza A/H1N1/2009 in Vietnam that utilises data from the cohort. Highly pathogenic avian influenza A/H5N1 remains endemic in poultry in parts of Southeast Asia and continues to infect humans. Marked familial clustering of human H5N1 cases has led to speculation that susceptibility to H5N1 infection may have a host genetic component. The epidemiological data that led to the hypothesis of genetic susceptibility to H5N1 is summarised, whilst the evidence for a role of host genetics in susceptibility to influenza in general is systematically reviewed. A genome-wide case-control genetic association study was conducted in Vietnam and Thailand to test the hypothesis of genetic susceptibility to H5N1 infection, and the results are presented. This work provides new data and understanding of the patterns and determinants of inter-pandemic, pandemic, and avian influenza epidemiology. The cohort study has added to the body of knowledge that is accruing on the burden and epidemiology of influenza in the tropics by providing community level data that were previously absent. The genetics study has provided the first direct evidence of genetic loci associated with susceptibility to H5N1 and opens new avenues of research to test these findings and their relevance to the pathogenesis of H5N1 and other types of influenza.